Hi,
I only know about one way, but it involves the need to purchase a external program called TransDEM - search the forum for detail about the program.
I have used it my self some years ago to lower a huge route by 1500 meter to get around the height limitations in Trainz with the -3000 to +3000 meter height range where all ground outside of that can't be easily worked on.
Having a route with Pike's Peak on it with up to about 4200 meter I got issues...
TransDEM made the changes quite nicely as I remember, but the route is no more of other reason.
The program changed all the ground, tracks, scenery items and splines and all, as far as I could tell it worked perfect.
Best wishes
Linda